{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T05:49:59Z","timestamp":1782280199603,"version":"3.54.5"},"posted":{"date-parts":[[2024,2,5]]},"group-title":"Genomics","reference-count":135,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2024,2,5]],"date-time":"2024-02-05T00:00:00Z","timestamp":1707091200000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2025,3,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>Studies in laboratory models and postmortem human brain tissue from patients with Alzheimer\u2019s disease have revealed disruption of basic cellular processes such as DNA repair and epigenetic control as drivers of neurodegeneration. While genomic alterations in regions of the genome that are rich in repetitive sequences, often termed \u201cdark regions,\u201d are difficult to resolve using traditional sequencing approaches, long-read technologies offer promising new avenues to explore previously inaccessible regions of the genome. In the current study, we leverage nanopore-based long-read whole-genome sequencing of DNA extracted from postmortem human frontal cortex at early and late stages of Alzheimer\u2019s disease, as well as age-matched controls, to analyze retrotransposon insertion events, non-allelic homologous recombination (NAHR), structural variants and DNA methylation within retrotransposon loci and other repetitive\/dark regions of the human genome. Interestingly, we find that retrotransposon insertion events and repetitive element-associated NAHR are particularly enriched within centromeric and pericentromeric regions of DNA in the aged human brain, and that ribosomal DNA (rDNA) is subject to a high degree of NAHR compared to other regions of the genome. We detect a trending increase in potential somatic retrotransposition events of the small interfering nuclear element (SINE) AluY in late-stage Alzheimer\u2019s disease, and differential changes in methylation within repetitive elements and retrotransposons according to disease stage. Taken together, our analysis provides the first long-read DNA sequencing-based analysis of retrotransposon sequences, NAHR, structural variants, and DNA methylation in the aged brain, and points toward transposable elements, centromeric\/pericentromeric regions and rDNA as hotspots for genomic variation.<\/jats:p>","DOI":"10.1101\/2024.02.01.578450","type":"posted-content","created":{"date-parts":[[2024,2,5]],"date-time":"2024-02-05T22:50:16Z","timestamp":1707173416000},"source":"Crossref","is-referenced-by-count":6,"title":["Nanopore Long-Read Sequencing Unveils Genomic Disruptions in Alzheimer\u2019s Disease"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8532-9590","authenticated-orcid":false,"given":"Paulino","family":"Ramirez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3186-5002","authenticated-orcid":false,"given":"Wenyan","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0349-4360","authenticated-orcid":false,"given":"Shiva Kazempour","family":"Dehkordi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5902-6238","authenticated-orcid":false,"given":"Habil","family":"Zare","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9225-0458","authenticated-orcid":false,"given":"Giovanni","family":"Pascarella","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7202-7243","authenticated-orcid":false,"given":"Piero","family":"Carninci","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8161-1553","authenticated-orcid":false,"given":"Bernard","family":"Fongang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4922-864X","authenticated-orcid":false,"given":"Kevin F.","family":"Bieniek","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1212-8138","authenticated-orcid":false,"given":"Bess","family":"Frost","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2025030600400708000_2024.02.01.578450v2.1","doi-asserted-by":"publisher","DOI":"10.3390\/genes12071071"},{"key":"2025030600400708000_2024.02.01.578450v2.2","doi-asserted-by":"publisher","DOI":"10.1002\/cne.22436"},{"key":"2025030600400708000_2024.02.01.578450v2.3","doi-asserted-by":"publisher","DOI":"10.1101\/gr.198937.115"},{"key":"2025030600400708000_2024.02.01.578450v2.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2018.12.107"},{"key":"2025030600400708000_2024.02.01.578450v2.5","doi-asserted-by":"publisher","DOI":"10.1093\/aje\/kwf074"},{"key":"2025030600400708000_2024.02.01.578450v2.6","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-021-03542-y"},{"key":"2025030600400708000_2024.02.01.578450v2.7","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genet-110711-155616"},{"key":"2025030600400708000_2024.02.01.578450v2.8","doi-asserted-by":"publisher","DOI":"10.1016\/j.neuron.2014.12.028"},{"key":"2025030600400708000_2024.02.01.578450v2.9","doi-asserted-by":"publisher","DOI":"10.1038\/nn.4388"},{"key":"2025030600400708000_2024.02.01.578450v2.10","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2015.03.026"},{"key":"2025030600400708000_2024.02.01.578450v2.11","doi-asserted-by":"crossref","unstructured":"Frost, B. and J. Dubnau , The Role of Retrotransposons and Endogenous Retroviruses in Age-Dependent Neurodegenerative Disorders. Annual Review of Neuroscience, 2024. 47.","DOI":"10.1146\/annurev-neuro-082823-020615"},{"key":"2025030600400708000_2024.02.01.578450v2.12","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2005.02.028"},{"key":"2025030600400708000_2024.02.01.578450v2.13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pgen.1005016"},{"key":"2025030600400708000_2024.02.01.578450v2.14","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229401.117"},{"key":"2025030600400708000_2024.02.01.578450v2.15","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-014-0572-2"},{"key":"2025030600400708000_2024.02.01.578450v2.16","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1394"},{"key":"2025030600400708000_2024.02.01.578450v2.17","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2022.06.032"},{"key":"2025030600400708000_2024.02.01.578450v2.18","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-019-1727-y"},{"key":"2025030600400708000_2024.02.01.578450v2.19","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-53260-y"},{"key":"2025030600400708000_2024.02.01.578450v2.20","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-019-45839-z"},{"key":"2025030600400708000_2024.02.01.578450v2.21","doi-asserted-by":"publisher","DOI":"10.1186\/s13059-022-02601-5"},{"key":"2025030600400708000_2024.02.01.578450v2.22","doi-asserted-by":"publisher","DOI":"10.1186\/s40659-023-00455-0"},{"key":"2025030600400708000_2024.02.01.578450v2.23","doi-asserted-by":"publisher","DOI":"10.1038\/s41592-023-01932-w"},{"key":"2025030600400708000_2024.02.01.578450v2.24","doi-asserted-by":"crossref","unstructured":"Siudeja, K. , et al., Unraveling the features of somatic transposition in the Drosophila intestine. The EMBO Journal, 2021. 40(9).","DOI":"10.15252\/embj.2020106388"},{"key":"2025030600400708000_2024.02.01.578450v2.25","doi-asserted-by":"publisher","DOI":"10.1126\/science.abj5089"},{"key":"2025030600400708000_2024.02.01.578450v2.26","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1682"},{"key":"2025030600400708000_2024.02.01.578450v2.27","doi-asserted-by":"publisher","DOI":"10.1111\/acel.12349"},{"key":"2025030600400708000_2024.02.01.578450v2.28","doi-asserted-by":"publisher","DOI":"10.1038\/sj.onc.1205651"},{"key":"2025030600400708000_2024.02.01.578450v2.29","doi-asserted-by":"publisher","DOI":"10.1016\/j.neurobiolaging.2008.12.005"},{"key":"2025030600400708000_2024.02.01.578450v2.30","doi-asserted-by":"publisher","DOI":"10.1016\/j.neurobiolaging.2013.02.021"},{"key":"2025030600400708000_2024.02.01.578450v2.31","doi-asserted-by":"publisher","DOI":"10.1007\/s12035-016-0357-6"},{"key":"2025030600400708000_2024.02.01.578450v2.32","doi-asserted-by":"crossref","unstructured":"Zhang, L. , et al., Epigenome-wide meta-analysis of DNA methylation differences in prefrontal cortex implicates the immune processes in Alzheimer\u2019s disease. Nature Communications, 2020. 11(1).","DOI":"10.1038\/s41467-020-19791-w"},{"key":"2025030600400708000_2024.02.01.578450v2.33","doi-asserted-by":"publisher","DOI":"10.3233\/JAD-2012-111223"},{"key":"2025030600400708000_2024.02.01.578450v2.34","doi-asserted-by":"crossref","unstructured":"Watson, C.T. , et al., Genome-wide DNA methylation profiling in the superior temporal gyrus reveals epigenetic signatures associated with Alzheimer\u2019s disease. Genome Medicine, 2016. 8(1).","DOI":"10.1186\/s13073-015-0258-8"},{"key":"2025030600400708000_2024.02.01.578450v2.35","doi-asserted-by":"publisher","DOI":"10.1097\/NEN.0b013e318232a379"},{"key":"2025030600400708000_2024.02.01.578450v2.36","unstructured":"Association, A.s. 2023 Alzheimer\u2019s disease facts and figures. 2023."},{"key":"2025030600400708000_2024.02.01.578450v2.37","doi-asserted-by":"publisher","DOI":"10.1007\/BF00308809"},{"key":"2025030600400708000_2024.02.01.578450v2.38","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2020.10.024"},{"key":"2025030600400708000_2024.02.01.578450v2.39","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2019.02.050"},{"key":"2025030600400708000_2024.02.01.578450v2.40","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)81997-2"},{"key":"2025030600400708000_2024.02.01.578450v2.41","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.94.5.1872"},{"key":"2025030600400708000_2024.02.01.578450v2.42","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2019.02.036"},{"key":"2025030600400708000_2024.02.01.578450v2.43","doi-asserted-by":"publisher","DOI":"10.1021\/bi981858s"},{"key":"2025030600400708000_2024.02.01.578450v2.44","doi-asserted-by":"crossref","unstructured":"Konkel, M.K. , et al., Sequence analysis and characterization of active human Alu subfamilies based on the 1000 Genomes Pilot Project. Genome Biology and Evolution, 2015: p. evv167.","DOI":"10.1093\/gbe\/evv167"},{"key":"2025030600400708000_2024.02.01.578450v2.45","doi-asserted-by":"publisher","DOI":"10.1101\/gad.191049.112"},{"key":"2025030600400708000_2024.02.01.578450v2.46","doi-asserted-by":"publisher","DOI":"10.1038\/nrg.2017.7"},{"key":"2025030600400708000_2024.02.01.578450v2.47","doi-asserted-by":"publisher","DOI":"10.1007\/s10577-017-9569-5"},{"key":"2025030600400708000_2024.02.01.578450v2.48","doi-asserted-by":"publisher","DOI":"10.1002\/dneu.22567"},{"key":"2025030600400708000_2024.02.01.578450v2.49","doi-asserted-by":"publisher","DOI":"10.1038\/nature03663"},{"key":"2025030600400708000_2024.02.01.578450v2.50","doi-asserted-by":"publisher","DOI":"10.1038\/nature10531"},{"key":"2025030600400708000_2024.02.01.578450v2.51","doi-asserted-by":"publisher","DOI":"10.1007\/s11033-021-06258-4"},{"key":"2025030600400708000_2024.02.01.578450v2.52","doi-asserted-by":"publisher","DOI":"10.1101\/gr.205701"},{"key":"2025030600400708000_2024.02.01.578450v2.53","doi-asserted-by":"publisher","DOI":"10.1016\/j.pneurobio.2021.102181"},{"key":"2025030600400708000_2024.02.01.578450v2.54","doi-asserted-by":"publisher","DOI":"10.1038\/s41593-018-0194-1"},{"key":"2025030600400708000_2024.02.01.578450v2.55","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2018.05.004"},{"key":"2025030600400708000_2024.02.01.578450v2.56","doi-asserted-by":"publisher","DOI":"10.3390\/ijms241311144"},{"key":"2025030600400708000_2024.02.01.578450v2.57","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-genom-082509-141802"},{"key":"2025030600400708000_2024.02.01.578450v2.58","doi-asserted-by":"publisher","DOI":"10.1002\/gcc.10111"},{"key":"2025030600400708000_2024.02.01.578450v2.59","doi-asserted-by":"publisher","DOI":"10.1016\/S0092-8674(00)80493-6"},{"key":"2025030600400708000_2024.02.01.578450v2.60","doi-asserted-by":"publisher","DOI":"10.1101\/gr.907603"},{"key":"2025030600400708000_2024.02.01.578450v2.61","doi-asserted-by":"publisher","DOI":"10.4161\/fly.19695"},{"key":"2025030600400708000_2024.02.01.578450v2.62","doi-asserted-by":"publisher","DOI":"10.1038\/ng0795-344"},{"key":"2025030600400708000_2024.02.01.578450v2.63","doi-asserted-by":"publisher","DOI":"10.1038\/S41588-018-0311-9"},{"key":"2025030600400708000_2024.02.01.578450v2.64","doi-asserted-by":"crossref","unstructured":"Kawatani, K. , et al., ABCA7 deficiency causes neuronal dysregulation by altering mitochondrial lipid metabolism. Molecular Psychiatry, 2023.","DOI":"10.1038\/s41380-023-02372-w"},{"key":"2025030600400708000_2024.02.01.578450v2.65","doi-asserted-by":"crossref","unstructured":"Fu, Y. , et al., Sex-specific lipid dysregulation in the Abca7 knockout mouse brain. Brain Communications, 2022. 4(3).","DOI":"10.1093\/braincomms\/fcac120"},{"key":"2025030600400708000_2024.02.01.578450v2.66","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.4165-12.2013"},{"key":"2025030600400708000_2024.02.01.578450v2.67","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.3757-15.2016"},{"key":"2025030600400708000_2024.02.01.578450v2.68","doi-asserted-by":"publisher","DOI":"10.1074\/jbc.M115.655076"},{"key":"2025030600400708000_2024.02.01.578450v2.69","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw124"},{"key":"2025030600400708000_2024.02.01.578450v2.70","doi-asserted-by":"crossref","unstructured":"Li, Q.S. , Y. Sun , and T. Wang , Epigenome-wide association study of Alzheimer\u2019s disease replicates 22 differentially methylated positions and 30 differentially methylated regions. Clinical Epigenetics, 2020. 12(1).","DOI":"10.1186\/s13148-020-00944-z"},{"key":"2025030600400708000_2024.02.01.578450v2.71","doi-asserted-by":"crossref","unstructured":"Pellegrini, C. , et al., A Meta-Analysis of brain DNA methylation across sex, age, and Alzheimer\u2019s Disease points for accelerated epigenetic aging in neurodegeneration. Frontiers in Aging Neuroscience, 2021. 13.","DOI":"10.3389\/fnagi.2021.639428"},{"key":"2025030600400708000_2024.02.01.578450v2.72","doi-asserted-by":"crossref","unstructured":"Smith, R.G. , et al., A meta-analysis of epigenome-wide association studies in Alzheimer\u2019s disease highlights novel differentially methylated loci across cortex. Nature Communications, 2021. 12(1).","DOI":"10.1038\/s41467-021-23243-4"},{"key":"2025030600400708000_2024.02.01.578450v2.73","doi-asserted-by":"publisher","DOI":"10.1007\/s40484-019-0183-8"},{"key":"2025030600400708000_2024.02.01.578450v2.74","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0022585"},{"key":"2025030600400708000_2024.02.01.578450v2.75","doi-asserted-by":"publisher","DOI":"10.1038\/ng1990"},{"key":"2025030600400708000_2024.02.01.578450v2.76","doi-asserted-by":"publisher","DOI":"10.1101\/gr.4362006"},{"key":"2025030600400708000_2024.02.01.578450v2.77","doi-asserted-by":"publisher","DOI":"10.1038\/nature13760"},{"key":"2025030600400708000_2024.02.01.578450v2.78","doi-asserted-by":"publisher","DOI":"10.1038\/nature21683"},{"key":"2025030600400708000_2024.02.01.578450v2.79","doi-asserted-by":"publisher","DOI":"10.1177\/1533317513505132"},{"key":"2025030600400708000_2024.02.01.578450v2.80","doi-asserted-by":"publisher","DOI":"10.1016\/j.bbi.2011.01.017"},{"key":"2025030600400708000_2024.02.01.578450v2.81","doi-asserted-by":"crossref","unstructured":"Ohtani, H. , et al., Efficient activation of hundreds of LTR12C elements reveals cis-regulatory function determined by distinct epigenetic mechanisms. Nucleic Acids Research, 2024: p. gkae498.","DOI":"10.1093\/nar\/gkae498"},{"key":"2025030600400708000_2024.02.01.578450v2.82","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2019.05.024"},{"key":"2025030600400708000_2024.02.01.578450v2.83","doi-asserted-by":"publisher","DOI":"10.20892\/j.issn.2095-3941.2016.0080"},{"key":"2025030600400708000_2024.02.01.578450v2.84","doi-asserted-by":"crossref","unstructured":"Gao, Y. , X.-F. Yu , and T. Chen , Human endogenous retroviruses in cancer: expression, regulation and function. Oncology Letters, 2020. 21(2).","DOI":"10.3892\/ol.2020.12382"},{"key":"2025030600400708000_2024.02.01.578450v2.85","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0076472"},{"key":"2025030600400708000_2024.02.01.578450v2.86","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty191"},{"key":"2025030600400708000_2024.02.01.578450v2.87","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx699"},{"key":"2025030600400708000_2024.02.01.578450v2.88","doi-asserted-by":"publisher","DOI":"10.1101\/gr.113985.110"},{"key":"2025030600400708000_2024.02.01.578450v2.89","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv1189"},{"key":"2025030600400708000_2024.02.01.578450v2.90","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.1990.9999"},{"key":"2025030600400708000_2024.02.01.578450v2.91","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac247"},{"key":"2025030600400708000_2024.02.01.578450v2.92","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1003118"},{"key":"2025030600400708000_2024.02.01.578450v2.93","doi-asserted-by":"publisher","DOI":"10.1093\/BIOINFORMATICS\/BTX183"},{"key":"2025030600400708000_2024.02.01.578450v2.94","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq033"},{"key":"2025030600400708000_2024.02.01.578450v2.95","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.1754"},{"key":"2025030600400708000_2024.02.01.578450v2.96","doi-asserted-by":"crossref","unstructured":"Bao, W. , K.K. Kojima , and O. Kohany , Repbase Update, a database of repetitive elements in eukaryotic genomes. Mobile DNA, 2015. 6(1).","DOI":"10.1186\/s13100-015-0041-9"},{"key":"2025030600400708000_2024.02.01.578450v2.97","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.3444"},{"key":"2025030600400708000_2024.02.01.578450v2.98","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2012-13-10-r87"},{"key":"2025030600400708000_2024.02.01.578450v2.99","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1009524"},{"key":"2025030600400708000_2024.02.01.578450v2.100","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkz107"},{"key":"2025030600400708000_2024.02.01.578450v2.101","doi-asserted-by":"crossref","unstructured":"Fishilevich, S. , et al., GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. Database, 2017. 2017.","DOI":"10.1093\/database\/bax028"},{"key":"2025030600400708000_2024.02.01.578450v2.102","doi-asserted-by":"publisher","DOI":"10.1101\/gr.229102. Article published online before print in May 2002"},{"key":"2025030600400708000_2024.02.01.578450v2.103","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv562"},{"key":"2025030600400708000_2024.02.01.578450v2.104","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2287-8"},{"key":"2025030600400708000_2024.02.01.578450v2.105","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkac128"},{"key":"2025030600400708000_2024.02.01.578450v2.106","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.27"},{"issue":"3","key":"2025030600400708000_2024.02.01.578450v2.107","doi-asserted-by":"crossref","first-page":"100141","DOI":"10.1016\/j.xinn.2021.100141","article-title":"clusterProfiler 4.0: A universal enrichment tool for interpreting omics data","volume":"2","year":"2021","journal-title":"The Innovation"},{"key":"2025030600400708000_2024.02.01.578450v2.108","doi-asserted-by":"crossref","unstructured":"Wickham, H. , ggplot2. Use R!, 2016.","DOI":"10.1007\/978-3-319-24277-4"},{"key":"2025030600400708000_2024.02.01.578450v2.109","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btv612"},{"key":"2025030600400708000_2024.02.01.578450v2.110","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx346"},{"key":"2025030600400708000_2024.02.01.578450v2.111","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-024-07278-3"},{"key":"2025030600400708000_2024.02.01.578450v2.112","doi-asserted-by":"publisher","DOI":"10.1038\/nn.3639"},{"key":"2025030600400708000_2024.02.01.578450v2.113","doi-asserted-by":"publisher","DOI":"10.1038\/s41593-018-0291-1"},{"key":"2025030600400708000_2024.02.01.578450v2.114","doi-asserted-by":"publisher","DOI":"10.1016\/j.stem.2021.04.004"},{"key":"2025030600400708000_2024.02.01.578450v2.115","doi-asserted-by":"publisher","DOI":"10.1016\/j.celrep.2016.02.048"},{"key":"2025030600400708000_2024.02.01.578450v2.116","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gky442"},{"key":"2025030600400708000_2024.02.01.578450v2.117","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2015.07.019"},{"key":"2025030600400708000_2024.02.01.578450v2.118","doi-asserted-by":"publisher","DOI":"10.1186\/1759-8753-1-1"},{"key":"2025030600400708000_2024.02.01.578450v2.119","doi-asserted-by":"publisher","DOI":"10.1111\/acel.14245"},{"key":"2025030600400708000_2024.02.01.578450v2.120","doi-asserted-by":"publisher","DOI":"10.1523\/JNEUROSCI.3029-15.2016"},{"key":"2025030600400708000_2024.02.01.578450v2.121","doi-asserted-by":"publisher","DOI":"10.1186\/s40478-021-01208-4"},{"key":"2025030600400708000_2024.02.01.578450v2.122","doi-asserted-by":"publisher","DOI":"10.1007\/s00401-019-01970-9"},{"key":"2025030600400708000_2024.02.01.578450v2.123","doi-asserted-by":"crossref","unstructured":"Dawson, T. , et al., Locus specific endogenous retroviral expression associated with Alzheimer\u2019s disease. Frontiers in Aging Neuroscience, 2023. 15.","DOI":"10.3389\/fnagi.2023.1186470"},{"key":"2025030600400708000_2024.02.01.578450v2.124","doi-asserted-by":"publisher","DOI":"10.1007\/s11357-022-00580-w"},{"key":"2025030600400708000_2024.02.01.578450v2.125","doi-asserted-by":"crossref","unstructured":"Scopa, C. , et al., JUN upregulation drives aberrant transposable element mobilization, associated innate immune response, and impaired neurogenesis in Alzheimer\u2019s disease. Nature Communications, 2023. 14(1).","DOI":"10.1038\/s41467-023-43728-8"},{"key":"2025030600400708000_2024.02.01.578450v2.126","doi-asserted-by":"crossref","unstructured":"Wahl, D. , et al., The reverse transcriptase inhibitor 3TC protects against age-related cognitive dysfunction. Aging Cell, 2023. 22(5).","DOI":"10.1111\/acel.13798"},{"key":"2025030600400708000_2024.02.01.578450v2.127","doi-asserted-by":"publisher","DOI":"10.15252\/embr.201642743"},{"key":"2025030600400708000_2024.02.01.578450v2.128","doi-asserted-by":"publisher","DOI":"10.1016\/j.molcel.2016.03.029"},{"key":"2025030600400708000_2024.02.01.578450v2.129","doi-asserted-by":"publisher","DOI":"10.1016\/j.gene.2009.06.020"},{"key":"2025030600400708000_2024.02.01.578450v2.130","doi-asserted-by":"publisher","DOI":"10.1038\/nrg2640"},{"key":"2025030600400708000_2024.02.01.578450v2.131","doi-asserted-by":"publisher","DOI":"10.1007\/s00401-024-02835-6"},{"key":"2025030600400708000_2024.02.01.578450v2.132","doi-asserted-by":"crossref","unstructured":"Wang, H. , et al., The role of structural variations in Alzheimer\u2019s disease and other neurodegenerative diseases. Frontiers in Aging Neuroscience, 2023. 14.","DOI":"10.3389\/fnagi.2022.1073905"},{"key":"2025030600400708000_2024.02.01.578450v2.133","doi-asserted-by":"publisher","DOI":"10.3390\/ijms22094603"},{"key":"2025030600400708000_2024.02.01.578450v2.134","doi-asserted-by":"publisher","DOI":"10.1007\/s00401-018-1841-z"},{"key":"2025030600400708000_2024.02.01.578450v2.135","doi-asserted-by":"crossref","unstructured":"Mastrorosa, F.K. , D.E. Miller , and E.E. Eichler , Applications of long-read sequencing to Mendelian genetics. Genome Medicine, 2023. 15(1).","DOI":"10.1186\/s13073-023-01194-3"}],"container-title":[],"original-title":[],"link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1101\/2024.02.01.578450","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,6,24]],"date-time":"2026-06-24T04:58:42Z","timestamp":1782277122000},"score":1,"resource":{"primary":{"URL":"http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/2024.02.01.578450"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,5]]},"references-count":135,"URL":"https:\/\/doi.org\/10.1101\/2024.02.01.578450","relation":{"is-preprint-of":[{"id-type":"doi","id":"10.1002\/alz.70852","asserted-by":"subject"}]},"subject":[],"published":{"date-parts":[[2024,2,5]]},"subtype":"preprint"}}